Journal Clubs

Chikashi Terao recalls a paper by Loh et al., which introduced a highly sensitive algorithm to detect low-fraction chromosomal mosaicism from SNP array data, enabling large-scale mapping of clonal haematopoiesis.

In this Journal Club, Fumitaka Inoue discusses a 2009 paper by Patwardhan et al. that introduced a massively parallel saturation-mutagenesis assay that leverages high-throughput DNA synthesis and sequencing to quantify the effects of single-nucleotide changes on regulatory element activity.

In this Journal Club, Angela Ruohao Wu highlights a 2012 paper by Karr et al. that exemplifies the value of 'rule-based' mechanistic models in biology, prompting questions about the future of predictive biological modelling in the current era of artificial intelligence.

Campbell and Goyal discuss a recent study by Rossine et al., which introduces a synthetic plasmid system that experimentally separates within-cell from between-cell selection, revealing multilevel evolutionary conflict and addressing questions first posed by Szathmáry and Smith in 1995.

In this Journal Club, Daniel Masiga recalls a 1986 publication by C. H. Green, which revealed how colour and odour cues influence tsetse fly (Glossina spp.) attraction, and a 2019 study by Attardo et al. on genomic insights across six Glossina species, advancing understanding of vector behaviour and control.

In this Journal Club, Hodkinson and Larschan recall a 2002 paper by Meller and Rattner that used the power of Drosophila genetics to demonstrate the integral role of long non-coding RNAs in dosage compensation.

In this Journal Club, Valborg Gudmundsdottir recalls a study by Menche et al., who used a network-based approach to systematically identify clusters of connections between disease-related proteins and elucidate the molecular underpinnings of disease–disease relationships.

In this Journal Club article, David Brückner discusses how seminal molecular genetic studies by Driever and Nüsslein-Volhard and Sick et al. demonstrated that both instructed (Wolpert model) and self-organized (Turing model) patterning occurs during animal development.

In this Journal Club, Nozomu Yachie recalls a 1999 paper by Pellegrini, Marcotte and colleagues that demonstrated how functional information, such as protein--protein interactions, could be revealed through patterns of genetic diversity across species.

In this Journal Club, Peter Koo reflects on the 2021 publication of Enformer and its impact on the use of deep learning for modelling the regulatory genome.

Jaime Martinez-Urtaza reflects on two papers by Smith et al., who found that bacteria exist along a continuum from clonal to recombining populations, and introduced the concept of an ‘epidemic’ microbial population structure.

In this Journal Club, Luis Orellana recalls a 2005 publication by Konstantinidis and Tiedje that introduced average nucleotide identity as a sequence-based metric to determine the relatedness between two genomes, which helped to operationally define bacterial species.

Jean Fan recounts a 2015 paper by Martincorena et al. that revealed oncogenic mutations in normal tissues, also highlighting how the latest spatial technologies can now be used to study the spatial contextual impact of these mutations.

In this Journal Club, Tzachi Hagai highlights a 2005 paper by Sawyer et al. that tested the functional relationship of evolutionary changes in immune genes with infection outcomes.

Sara Suliman describes a seminal 2013 publication by Comas et al. that investigated the origins of the tuberculosis-causing bacteria and its coevolution with diverse human populations.

Gerald Mboowa reflects on the dual legacy of a 2021 study by Frangoul et al., which demonstrated safe and effective CRISPR-based editing to treat sickle-cell disease and β-thalassemia, as both a triumph of modern science and a call to action for global health.

Daudi Jjingo highlights a recent publication by Chu et al., who performed an integrative single-cell analysis of human colorectal cancer to characterize the tumour microenvironment (TME) and stratify patients according to their heterogeneous TMEs, which exploit different immune evasion mechanisms.

In this Journal Club, Chikara Furusawa reflects on a 1991 publication by Tom Ray that presented Tierra, an evolvable computer program that pioneered the use of artificial life to study biological phenomena.

Samira Musah highlights a recent study by Ward et al., who generated isogenic human induced pluripotent stem cell lines to analyse the transcriptional and epigenetic effects of SMAD2 variants identified in patients with congenital heart disease.

In this Journal Club, Josué Barrera-Redondo and Susana Coelho recount a 2012 paper by Carvunis et al. that provided a powerful framework for studying de novo gene evolution.